Let's take a step back; in which application exactly are you seeing this?

And the space set aside for administrative purposes is fixed; meaning it needs the same amount of space even with zero files or with a million files. That is how the ext4 filesystem works, upon creation a portion of the disk is set aside for administrative purposes. That said, 5% does sound a bit much perhaps--on my 240 GB hard disk it is closer to 2%.

So for example when a hard disk manufacturer states he has a 1 TB hard disk, most applications will show that as 0.91 TiB. That is the same amount of bytes, but with a different notation. It's quite a difference, and may also here be clouding the figures you are looking at.

xenopeek: check "man tune2fs" regarding the "-m" option This space is reported as used (unavailable), even if it is empty, with df in a term, with gparted or with gnome-system-monitor (in GSM: compute "free space" minus "available space" while "used space" percentage is computed on what remains "available")